PDBsum entry 2jp9

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protein dna_rna metals links
Transcription/DNA PDB id
Protein chain
119 a.a. *
_ZN ×4
* Residue conservation analysis
PDB id:
Name: Transcription/DNA
Title: Structure of the wilms tumor suppressor protein zinc finger domain bound to DNA
Structure: Wilms tumor 1. Chain: a. Fragment: residues 174-291. Engineered: yes. DNA (5'- d(p Dcp Dgp Dcp Dgp Dgp Dgp Dgp Dgp Dcp Dgp Dtp Dcp Dtp Dgp Dcp Dgp Dc)-3'). Chain: b. Engineered: yes.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: wt1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes
NMR struc: 20 models
Authors: R.Stoll,B.M.Lee,E.W.Debler,J.H.Laity,I.A.Wilson,H.J.Dyson, P.E.Wright
Key ref:
R.Stoll et al. (2007). Structure of the wilms tumor suppressor protein zinc finger domain bound to DNA. J Mol Biol, 372, 1227-1245. PubMed id: 17716689 DOI: 10.1016/j.jmb.2007.07.017
30-Apr-07     Release date:   30-Oct-07    
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Protein chain
Pfam   ArchSchema ?
P19544  (WT1_HUMAN) -  Wilms tumor protein
449 a.a.
119 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleic acid binding     2 terms  


DOI no: 10.1016/j.jmb.2007.07.017 J Mol Biol 372:1227-1245 (2007)
PubMed id: 17716689  
Structure of the wilms tumor suppressor protein zinc finger domain bound to DNA.
R.Stoll, B.M.Lee, E.W.Debler, J.H.Laity, I.A.Wilson, H.J.Dyson, P.E.Wright.
The zinc finger domain of the Wilms tumor suppressor protein (WT1) contains four canonical Cys(2)His(2) zinc fingers. WT1 binds preferentially to DNA sequences that are closely related to the EGR-1 consensus site. We report the structure determination by both X-ray crystallography and NMR spectroscopy of the WT1 zinc finger domain in complex with DNA. The X-ray structure was determined for the complex with a cognate 14 base-pair oligonucleotide, and composite X-ray/NMR structures were determined for complexes with both the 14 base-pair and an extended 17 base-pair DNA. This combined approach allowed unambiguous determination of the position of the first zinc finger, which is influenced by lattice contacts in the crystal structure. The crystal structure shows the second, third and fourth zinc finger domains inserted deep into the major groove of the DNA where they make base-specific interactions. The DNA duplex is distorted in the vicinity of the first zinc finger, with a cytidine twisted and tilted out of the base stack to pack against finger 1 and the tip of finger 2. By contrast, the composite X-ray/NMR structures show that finger 1 continues to follow the major groove in the solution complexes. However, the orientation of the helix is non-canonical, and the fingertip and the N terminus of the helix project out of the major groove; as a consequence, the zinc finger side-chains that are commonly involved in base recognition make no contact with the DNA. We conclude that finger 1 helps to anchor WT1 to the DNA by amplifying the binding affinity although it does not contribute significantly to binding specificity. The structures provide molecular level insights into the potential consequences of mutations in zinc fingers 2 and 3 that are associated with Denys-Drash syndrome and nephritic syndrome. The mutations are of two types, and either destabilize the zinc finger structure or replace key base contact residues.
  Selected figure(s)  
Figure 5.
Figure 5. Close-up view of contacts observed in the X-ray crystal structure. (a) Interactions between Arg394 (dark blue) and Asp396 (red) of finger 3 (pink) and the bases of GUA7 (gray) and CYT29 (green) of the 14 bp DNA duplex. (b) Interactions between Arg366 (dark blue) of finger 2 (blue-green) and the bases of ADE26 (red), CYT9 (purple), GUA10 (light blue) and THY11 (green).
Figure 10.
Figure 10. Stereo view of a superposition of the X-ray structure (colors as for Figure 2), the NMR/X-ray solution structure of zf1-4 with the 14 bp DNA duplex (colors medium blue, medium blue-green, maroon and tan for fingers 1–4, respectively) and the NMR/X-ray structure of zf1-4 with the 17 bp DNA duplex (colors dark blue, dark green, dark maroon and brown for fingers 1–4, respectively). The coding and non-coding strands of the DNA are shown in gold and orange, respectively, except for the 5′ end of the non-coding strand of the X-ray structure, which is shown in red.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 372, 1227-1245) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21248786 V.Huff (2011).
Wilms' tumours: about tumour suppressor genes, an oncogene and a chameleon gene.
  Nat Rev Cancer, 11, 111-121.  
20565873 C.C.Chou, M.Rajasekaran, and C.Chen (2010).
An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking.
  BMC Bioinformatics, 11, 334.  
20544958 C.C.Chou, Y.C.Lou, T.K.Tang, and C.Chen (2010).
Structure and DNA binding characteristics of the three-Cys(2)His(2) domain of mouse testis zinc finger protein.
  Proteins, 78, 2202-2212.  
20563762 G.Kock, M.Dicks, R.Heumann, K.S.Erdmann, and R.Stoll (2010).
Sequence-specific 1H, 13C, and 15N assignment of the extended PDZ3 domain of the protein tyrosine phosphatase basophil-like PTP-BL.
  Biomol NMR Assign, 4, 199-202.  
20167128 M.Hatayama, and J.Aruga (2010).
Characterization of the tandem CWCH2 sequence motif: a hallmark of inter-zinc finger interactions.
  BMC Evol Biol, 10, 53.  
20685651 S.Karassek, C.Berghaus, M.Schwarten, C.G.Goemans, N.Ohse, G.Kock, K.Jockers, S.Neumann, S.Gottfried, C.Herrmann, R.Heumann, and R.Stoll (2010).
Ras homolog enriched in brain (Rheb) enhances apoptotic signaling.
  J Biol Chem, 285, 33979-33991.
PDB code: 2l0x
19221039 V.I.Gaidzik, R.F.Schlenk, S.Moschny, A.Becker, L.Bullinger, A.Corbacioglu, J.Krauter, B.Schlegelberger, A.Ganser, H.Döhner, and K.Döhner (2009).
Prognostic impact of WT1 mutations in cytogenetically normal acute myeloid leukemia: a study of the German-Austrian AML Study Group.
  Blood, 113, 4505-4511.  
18559874 P.Paschka, G.Marcucci, A.S.Ruppert, S.P.Whitman, K.Mrózek, K.Maharry, C.Langer, C.D.Baldus, W.Zhao, B.L.Powell, M.R.Baer, A.J.Carroll, M.A.Caligiuri, J.E.Kolitz, R.A.Larson, and C.D.Bloomfield (2008).
Wilms' tumor 1 gene mutations independently predict poor outcome in adults with cytogenetically normal acute myeloid leukemia: a cancer and leukemia group B study.
  J Clin Oncol, 26, 4595-4602.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.